Table errors are almost certainly caused by something not being in the right order. The FS2 parser had a limited correcting ability, but really wasn't very smart at all. There were problems where a mod got lazy and released some tables with fields in the wrong order, causing crashes that appeared entirely unrelated.
If it really is just table errors, it's gonna simply be a matter of putting the fields in the correct order. They may not have broken FS2, but that could just be because they overwrote a virtually-unused portion of memory. Whereas in the SCP, that section of memory could be vital to something else.